\docType{methods}
\name{assocComp}
\alias{assocComp}
\title{Associate principal components with sample annotations}
\usage{
  assocComp(mBase, sampleAnnotation)
}
\arguments{
  \item{mBase}{\code{\link{methylBase}} object with no NA
  values in the data part.}

  \item{sampleAnnotation}{a data frame where columns are
  different annotations and rows are the samples, in the
  same order as in the methylBase object.}
}
\value{
  a named list of principal component matrix (named
  'pcs'),% variation explained by principal compopents
  (named 'vars') and a p-value matrix showing association
  p-values between sample annotations and principal
  components (named 'association').
}
\description{
  This function associates principal components with sample
  annotations such as age, gender, batch_id. Can be used to
  detect which batch effects are associated with the
  variation in the methylation values.
}
\examples{
data(methylKit)
sampleAnnotation=data.frame(batch_id=c("a","a","b","b"),age=c(19,34,23,40))
as=assocComp(mBase=methylBase.obj,sampleAnnotation)
}
\author{
  Altuna Akalin
}

